CCDC59

coiled-coil domain containing 59

Basic information

Region (hg38): 12:82223681-82358805

Links

ENSG00000133773 ∙ NCBI:29080 ∙ OMIM:619280 ∙ HGNC:25005 ∙ Uniprot:Q9P031 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CCDC59 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC59 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	0	0

Variants in CCDC59

This is a list of pathogenic ClinVar variants found in the CCDC59 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
12-82353164-T-G		not specified	Uncertain significance (Sep 14, 2022)
12-82353179-A-C		not specified	Uncertain significance (Apr 13, 2023)
12-82353189-T-C		not specified	Uncertain significance (Nov 08, 2022)
12-82353291-C-G		not specified	Uncertain significance (Dec 01, 2023)
12-82353312-C-T		not specified	Uncertain significance (Sep 26, 2022)
12-82357031-G-C		not specified	Uncertain significance (Sep 01, 2021)
12-82357087-G-C		not specified	Uncertain significance (Mar 19, 2024)
12-82357099-T-C		not specified	Uncertain significance (May 28, 2024)
12-82357146-A-G		not specified	Uncertain significance (Nov 23, 2021)
12-82357242-A-T		not specified	Uncertain significance (Nov 30, 2021)
12-82358229-G-A		not specified	Uncertain significance (Apr 07, 2022)
12-82358332-A-C		not specified	Uncertain significance (Apr 04, 2023)
12-82358343-G-A		not specified	Uncertain significance (Feb 13, 2024)
12-82358346-G-A		not specified	Uncertain significance (Aug 17, 2021)
12-82358361-G-C		not specified	Uncertain significance (Dec 01, 2022)
12-82358364-T-C		not specified	Uncertain significance (May 24, 2023)
12-82358570-C-T		not specified	Uncertain significance (Jun 23, 2023)
12-82358581-C-T		not specified	Uncertain significance (May 06, 2022)
12-82358602-C-G		not specified	Uncertain significance (Jan 23, 2024)
12-82358660-C-G		not specified	Uncertain significance (Feb 12, 2024)
12-82358690-A-G		not specified	Uncertain significance (Dec 14, 2021)
12-82358693-C-T		not specified	Uncertain significance (Jul 10, 2023)
12-82358716-G-C		not specified	Uncertain significance (Jan 31, 2024)
12-82358737-G-A		not specified	Uncertain significance (Oct 03, 2022)
12-82358746-G-T		not specified	Uncertain significance (Sep 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC59	protein_coding	protein_coding	ENST00000256151	4	135125

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.03e-11	0.0273	125349	0	399	125748	0.00159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.37	167	124	1.34	0.00000613	1583
Missense in Polyphen		47	38.116	1.2331		547
Synonymous	-0.968	56	47.5	1.18	0.00000250	416
Loss of Function	-0.426	15	13.3	1.13	6.97e-7	159

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00101	0.000985
Ashkenazi Jewish	0.00151	0.00139
East Asian	0.000604	0.000598
Finnish	0.00358	0.00342
European (Non-Finnish)	0.00248	0.00223
Middle Eastern	0.000604	0.000598
South Asian	0.000482	0.000425
Other	0.00198	0.00179

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the transcription complexes of the pulmonary surfactant-associated protein-B (SFTPB) and -C (SFTPC). Enhances homeobox protein Nkx-2.1-activated SFTPB and SFTPC promoter activities. {ECO:0000269|PubMed:12882447, ECO:0000269|PubMed:16630564}.
• Pathway: Surfactant metabolism;Metabolism of proteins (Consensus)

Recessive Scores

• pRec: 0.0959

Intolerance Scores

• loftool: 0.384
• rvis_EVS: 1.06
• rvis_percentile_EVS: 91.47

Haploinsufficiency Scores

• pHI: 0.341
• hipred: N
• hipred_score: 0.144

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.633

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Ccdc59

Gene ontology

• Biological process: cellular protein metabolic process
• Cellular component: nucleoplasm
• Molecular function: RNA binding;protein binding